K-mer Motif Multinomial Mixtures, a scalable framework for multiple motif discovery

1AbstractMotivationThe advent of inexpensive high-throughput sequencing (HTS) places new demands on motif discovery algorithms. To confront the challenges and embrace the opportunities presented by the growing wealth of information tied up in HTS datasets, we developed K-mer motif multinomial mixtures (KMMMs), a flexible class of Bayesian models for identifying multiple motifs in sequence sets using K-mer tables. Advantages of this framework are inference with time and space complexities that only scale with K, and the ability to be incorporated into larger Bayesian models.ResultsWe derived a class of probabilistic models of K-mer tables generated from sequence containing multiple motifs. KMMMs model the K-mer table as a multinomial mixture, with motif and background components, which are distributions over K-mers overlapping with each of the latent motifs and over K-mers that do not overlap with any motif, respectively. The framework casts motif discovery as a posterior inference problem, and we present several approximate inference methods that provide accurate reconstructions of motifs in synthetic data. Finally we apply the method to discover motifs in DNAse hypersensitive sites and ChIP-seq peaks obtained from the ENCODE project.

Texture Fusion for Batik Motif Retrieval System

<p>This paper systematically investigates the effect of image texture features on batik motif retrieval performance. The retrieval process uses a query motif image to find matching motif images in a database. In this study, feature fusion of various image texture features such as Gabor, Log-Gabor, Grey Level Co-Occurrence Matrices (GLCM), and Local Binary Pattern (LBP) features are attempted in motif image retrieval. With regards to performance evaluation, both individual features and fused feature sets are applied. Experimental results show that optimal feature fusion outperforms individual features in batik motif retrieval. Among the individual features tested, Log-Gabor features provide the best result. The proposed approach is best used in a scenario where a query image containing multiple basic motif objects is applied to a dataset in which retrieved images also contain multiple motif objects. The retrieval rate achieves 84.54% for the rank 3 precision when the feature space is fused with Gabor, GLCM and Log-Gabor features. The investigation also shows that the proposed method does not work well for a retrieval scenario where the query image contains multiple basic motif objects being applied to a dataset in which the retrieved images only contain one basic motif object.</p>

Texture Fusion for Batik Motif Retrieval System

<p>This paper systematically investigates the effect of image texture features on batik motif retrieval performance. The retrieval process uses a query motif image to find matching motif images in a database. In this study, feature fusion of various image texture features such as Gabor, Log-Gabor, Grey Level Co-Occurrence Matrices (GLCM), and Local Binary Pattern (LBP) features are attempted in motif image retrieval. With regards to performance evaluation, both individual features and fused feature sets are applied. Experimental results show that optimal feature fusion outperforms individual features in batik motif retrieval. Among the individual features tested, Log-Gabor features provide the best result. The proposed approach is best used in a scenario where a query image containing multiple basic motif objects is applied to a dataset in which retrieved images also contain multiple motif objects. The retrieval rate achieves 84.54% for the rank 3 precision when the feature space is fused with Gabor, GLCM and Log-Gabor features. The investigation also shows that the proposed method does not work well for a retrieval scenario where the query image contains multiple basic motif objects being applied to a dataset in which the retrieved images only contain one basic motif object.</p>

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

ABSTRACTTranscription Factor (TF) databases contain multitudes of motifs from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq peaks) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant collections of motifs. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools and highlights biologically relevant variations of similar motifs. By clustering 24 entire databases (>7,500 motifs), we show that matrix-clustering correctly groups motifs belonging to the same TF families, and can drastically reduce motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines.